HEADER OXIDOREDUCTASE 22-NOV-14 4D7D TITLE CYTOCHROME P450 3A4 BOUND TO AN INHIBITOR COMPND MOL_ID: 1; COMPND 2 MOLECULE: CYTOCHROME P450 3A4; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: CATALYTIC DOMAIN, UNP RESIDUES 23-503; COMPND 5 SYNONYM: 1,8-CINEOLE 2-EXO-MONOOXYGENASE, ALBENDAZOLE MONOOXYGENASE, COMPND 6 ALBENDAZOLE SULFOXIDASE, CYPIIIA3, CYPIIIA4, CYTOCHROME P450 3A3, COMPND 7 CYTOCHROME P450 HLP, CYTOCHROME P450 NF-25, CYTOCHROME P450-PCN1, COMPND 8 NIFEDIPINE OXIDASE, QUININE 3-MONOOXYGENASE, TAUROCHENODEOXYCHOLA TE COMPND 9 6-ALPHA-HYDROXYLASE; COMPND 10 EC: 1.14.13.157, 1.14.13.32, 1.14.13.67, 1.14.13.97; COMPND 11 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PCWORI KEYWDS OXIDOREDUCTASE, MONOOXYGENASE, HUMAN CYP3A4, INHIBITORY COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR I.SEVRIOUKOVA,T.POULOS REVDAT 5 20-DEC-23 4D7D 1 REMARK REVDAT 4 08-MAY-19 4D7D 1 REMARK REVDAT 3 25-MAY-16 4D7D 1 JRNL REVDAT 2 30-SEP-15 4D7D 1 JRNL REVDAT 1 23-SEP-15 4D7D 0 JRNL AUTH P.KAUR,R.CHAMBERLIN,T.L.POULOS,I.F.SEVRIOUKOVA JRNL TITL STRUCTURE-BASED INHIBITOR DESIGN FOR EVALUATION OF A CYP3A4 JRNL TITL 2 PHARMACOPHORE MODEL. JRNL REF J.MED.CHEM. V. 59 4210 2016 JRNL REFN ISSN 0022-2623 JRNL PMID 26371436 JRNL DOI 10.1021/ACS.JMEDCHEM.5B01146 REMARK 2 REMARK 2 RESOLUTION. 2.76 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.6 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.76 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 37.44 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.3 REMARK 3 NUMBER OF REFLECTIONS : 12401 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.204 REMARK 3 R VALUE (WORKING SET) : 0.200 REMARK 3 FREE R VALUE : 0.278 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 645 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.76 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.83 REMARK 3 REFLECTION IN BIN (WORKING SET) : 656 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 74.49 REMARK 3 BIN R VALUE (WORKING SET) : 0.3250 REMARK 3 BIN FREE R VALUE SET COUNT : 36 REMARK 3 BIN FREE R VALUE : 0.3560 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3689 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 76 REMARK 3 SOLVENT ATOMS : 10 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 109.1 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.05000 REMARK 3 B22 (A**2) : -0.05000 REMARK 3 B33 (A**2) : 0.00000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.000 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.435 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.380 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 41.794 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.964 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.925 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3863 ; 0.009 ; 0.020 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5240 ; 1.934 ; 2.013 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 455 ; 6.451 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 161 ;34.706 ;23.851 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 689 ;20.045 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 22 ;14.241 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 575 ; 0.097 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2879 ; 0.008 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 29 A 497 REMARK 3 ORIGIN FOR THE GROUP (A): -19.5430 23.9665 13.0517 REMARK 3 T TENSOR REMARK 3 T11: 0.1015 T22: 0.1980 REMARK 3 T33: 0.1049 T12: 0.0227 REMARK 3 T13: -0.0039 T23: -0.0427 REMARK 3 L TENSOR REMARK 3 L11: 2.1436 L22: 4.6299 REMARK 3 L33: 2.3950 L12: 1.3521 REMARK 3 L13: 0.6070 L23: 0.9822 REMARK 3 S TENSOR REMARK 3 S11: -0.1209 S12: -0.1248 S13: 0.2489 REMARK 3 S21: -0.5207 S22: 0.0174 S23: 0.0311 REMARK 3 S31: -0.3763 S32: -0.1712 S33: 0.1034 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS. RESIDUES 265-266 AND 281-288 ARE DISORDERED REMARK 4 REMARK 4 4D7D COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 22-NOV-14. REMARK 100 THE DEPOSITION ID IS D_1290062365. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 27-JUL-13 REMARK 200 TEMPERATURE (KELVIN) : 113 REMARK 200 PH : 5.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL11-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.98 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13205 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.760 REMARK 200 RESOLUTION RANGE LOW (A) : 37.400 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.3 REMARK 200 DATA REDUNDANCY : 9.600 REMARK 200 R MERGE (I) : 0.08000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.76 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.91 REMARK 200 COMPLETENESS FOR SHELL (%) : 89.0 REMARK 200 DATA REDUNDANCY IN SHELL : 8.00 REMARK 200 R MERGE FOR SHELL (I) : 1.50000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: PDB ENTRY 1TQN REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.47 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.53 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: MICROBATCH UNDER OIL WITH 11% PEG 3350 REMARK 280 AND 60 MM SODIUM MALONATE PH 5.0 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 2 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X,Y,-Z REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-Y+1/2,-Z+1/2 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 39.06900 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 50.66600 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 63.98300 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 39.06900 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 50.66600 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 63.98300 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 39.06900 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 50.66600 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 63.98300 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 39.06900 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 50.66600 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 63.98300 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 MET A 21 REMARK 465 ALA A 22 REMARK 465 TYR A 23 REMARK 465 LEU A 24 REMARK 465 TYR A 25 REMARK 465 GLY A 26 REMARK 465 THR A 27 REMARK 465 HIS A 28 REMARK 465 GLN A 265 REMARK 465 LYS A 266 REMARK 465 SER A 281 REMARK 465 LYS A 282 REMARK 465 GLU A 283 REMARK 465 THR A 284 REMARK 465 GLU A 285 REMARK 465 SER A 286 REMARK 465 HIS A 287 REMARK 465 LYS A 288 REMARK 465 GLY A 498 REMARK 465 THR A 499 REMARK 465 VAL A 500 REMARK 465 SER A 501 REMARK 465 GLY A 502 REMARK 465 ALA A 503 REMARK 465 HIS A 504 REMARK 465 HIS A 505 REMARK 465 HIS A 506 REMARK 465 HIS A 507 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 ASP A 497 CA C O CB CG OD1 OD2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 PRO A 169 C - N - CA ANGL. DEV. = 9.7 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 PHE A 46 -49.21 70.86 REMARK 500 VAL A 95 -58.62 -120.94 REMARK 500 VAL A 101 -57.03 -133.07 REMARK 500 ASP A 123 -133.71 39.60 REMARK 500 PRO A 135 -1.56 -59.28 REMARK 500 THR A 138 -165.75 -123.39 REMARK 500 PRO A 169 166.22 -44.81 REMARK 500 PRO A 199 29.64 -76.23 REMARK 500 PHE A 219 -70.22 -62.17 REMARK 500 VAL A 225 -16.84 144.02 REMARK 500 PHE A 226 54.19 -143.31 REMARK 500 PHE A 241 50.18 -155.65 REMARK 500 PRO A 242 84.30 -43.29 REMARK 500 ARG A 243 -21.52 72.98 REMARK 500 PHE A 248 -70.89 -54.44 REMARK 500 LEU A 261 -15.12 -43.28 REMARK 500 MET A 371 -55.93 71.64 REMARK 500 GLU A 410 67.06 38.22 REMARK 500 THR A 433 59.99 -141.23 REMARK 500 CYS A 468 -158.46 -129.26 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 ARG A 268 0.23 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 600 REMARK 600 HETEROGEN REMARK 600 REMARK 600 NEEDS TO BE NAMED (PKT): FIGURE WITH THE PKT STRUCTURE IS REMARK 600 ATTACHED REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 HEM A1500 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 442 SG REMARK 620 2 HEM A1500 NA 113.0 REMARK 620 3 HEM A1500 NB 94.2 84.1 REMARK 620 4 HEM A1500 NC 97.3 149.3 89.7 REMARK 620 5 HEM A1500 ND 101.6 87.6 164.0 90.5 REMARK 620 6 PKT A1600 N22 173.3 73.6 85.2 76.0 79.3 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HEM A 1500 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PKT A 1600 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4D6Z RELATED DB: PDB REMARK 900 CYTOCHROME P450 3A4 BOUND TO IMIDAZOLE AND AN INHIBITOR REMARK 900 RELATED ID: 4D75 RELATED DB: PDB REMARK 900 CYTOCHROME P450 3A4 BOUND TO AN INHIBITOR REMARK 900 RELATED ID: 4D78 RELATED DB: PDB REMARK 900 CYTOCHROME P450 3A4 BOUND TO AN INHIBITOR DBREF 4D7D A 23 503 UNP P08684 CP3A4_HUMAN 23 503 SEQADV 4D7D MET A 21 UNP P08684 EXPRESSION TAG SEQADV 4D7D ALA A 22 UNP P08684 EXPRESSION TAG SEQADV 4D7D HIS A 504 UNP P08684 EXPRESSION TAG SEQADV 4D7D HIS A 505 UNP P08684 EXPRESSION TAG SEQADV 4D7D HIS A 506 UNP P08684 EXPRESSION TAG SEQADV 4D7D HIS A 507 UNP P08684 EXPRESSION TAG SEQRES 1 A 487 MET ALA TYR LEU TYR GLY THR HIS SER HIS GLY LEU PHE SEQRES 2 A 487 LYS LYS LEU GLY ILE PRO GLY PRO THR PRO LEU PRO PHE SEQRES 3 A 487 LEU GLY ASN ILE LEU SER TYR HIS LYS GLY PHE CYS MET SEQRES 4 A 487 PHE ASP MET GLU CYS HIS LYS LYS TYR GLY LYS VAL TRP SEQRES 5 A 487 GLY PHE TYR ASP GLY GLN GLN PRO VAL LEU ALA ILE THR SEQRES 6 A 487 ASP PRO ASP MET ILE LYS THR VAL LEU VAL LYS GLU CYS SEQRES 7 A 487 TYR SER VAL PHE THR ASN ARG ARG PRO PHE GLY PRO VAL SEQRES 8 A 487 GLY PHE MET LYS SER ALA ILE SER ILE ALA GLU ASP GLU SEQRES 9 A 487 GLU TRP LYS ARG LEU ARG SER LEU LEU SER PRO THR PHE SEQRES 10 A 487 THR SER GLY LYS LEU LYS GLU MET VAL PRO ILE ILE ALA SEQRES 11 A 487 GLN TYR GLY ASP VAL LEU VAL ARG ASN LEU ARG ARG GLU SEQRES 12 A 487 ALA GLU THR GLY LYS PRO VAL THR LEU LYS ASP VAL PHE SEQRES 13 A 487 GLY ALA TYR SER MET ASP VAL ILE THR SER THR SER PHE SEQRES 14 A 487 GLY VAL ASN ILE ASP SER LEU ASN ASN PRO GLN ASP PRO SEQRES 15 A 487 PHE VAL GLU ASN THR LYS LYS LEU LEU ARG PHE ASP PHE SEQRES 16 A 487 LEU ASP PRO PHE PHE LEU SER ILE THR VAL PHE PRO PHE SEQRES 17 A 487 LEU ILE PRO ILE LEU GLU VAL LEU ASN ILE CYS VAL PHE SEQRES 18 A 487 PRO ARG GLU VAL THR ASN PHE LEU ARG LYS SER VAL LYS SEQRES 19 A 487 ARG MET LYS GLU SER ARG LEU GLU ASP THR GLN LYS HIS SEQRES 20 A 487 ARG VAL ASP PHE LEU GLN LEU MET ILE ASP SER GLN ASN SEQRES 21 A 487 SER LYS GLU THR GLU SER HIS LYS ALA LEU SER ASP LEU SEQRES 22 A 487 GLU LEU VAL ALA GLN SER ILE ILE PHE ILE PHE ALA GLY SEQRES 23 A 487 TYR GLU THR THR SER SER VAL LEU SER PHE ILE MET TYR SEQRES 24 A 487 GLU LEU ALA THR HIS PRO ASP VAL GLN GLN LYS LEU GLN SEQRES 25 A 487 GLU GLU ILE ASP ALA VAL LEU PRO ASN LYS ALA PRO PRO SEQRES 26 A 487 THR TYR ASP THR VAL LEU GLN MET GLU TYR LEU ASP MET SEQRES 27 A 487 VAL VAL ASN GLU THR LEU ARG LEU PHE PRO ILE ALA MET SEQRES 28 A 487 ARG LEU GLU ARG VAL CYS LYS LYS ASP VAL GLU ILE ASN SEQRES 29 A 487 GLY MET PHE ILE PRO LYS GLY VAL VAL VAL MET ILE PRO SEQRES 30 A 487 SER TYR ALA LEU HIS ARG ASP PRO LYS TYR TRP THR GLU SEQRES 31 A 487 PRO GLU LYS PHE LEU PRO GLU ARG PHE SER LYS LYS ASN SEQRES 32 A 487 LYS ASP ASN ILE ASP PRO TYR ILE TYR THR PRO PHE GLY SEQRES 33 A 487 SER GLY PRO ARG ASN CYS ILE GLY MET ARG PHE ALA LEU SEQRES 34 A 487 MET ASN MET LYS LEU ALA LEU ILE ARG VAL LEU GLN ASN SEQRES 35 A 487 PHE SER PHE LYS PRO CYS LYS GLU THR GLN ILE PRO LEU SEQRES 36 A 487 LYS LEU SER LEU GLY GLY LEU LEU GLN PRO GLU LYS PRO SEQRES 37 A 487 VAL VAL LEU LYS VAL GLU SER ARG ASP GLY THR VAL SER SEQRES 38 A 487 GLY ALA HIS HIS HIS HIS HET HEM A1500 43 HET PKT A1600 33 HETNAM HEM PROTOPORPHYRIN IX CONTAINING FE HETNAM PKT TERT-BUTYL [(2S)-1-(1H-INDOL-3-YL)-3-({3-OXO-3- HETNAM 2 PKT [(PYRIDIN-3-YLMETHYL)AMINO]PROPYL}SULFANYL)PROPAN-2- HETNAM 3 PKT YL]CARBAMATE HETSYN HEM HEME FORMUL 2 HEM C34 H32 FE N4 O4 FORMUL 3 PKT C25 H32 N4 O3 S FORMUL 4 HOH *10(H2 O) HELIX 1 1 GLY A 31 LEU A 36 1 6 HELIX 2 2 ASN A 49 LYS A 55 5 7 HELIX 3 3 GLY A 56 GLY A 69 1 14 HELIX 4 4 ASP A 86 VAL A 95 1 10 HELIX 5 5 VAL A 111 ALA A 117 5 7 HELIX 6 6 GLU A 122 SER A 134 1 13 HELIX 7 7 PRO A 135 PHE A 137 5 3 HELIX 8 8 THR A 138 GLU A 144 1 7 HELIX 9 9 MET A 145 GLY A 167 1 23 HELIX 10 10 LEU A 172 GLY A 190 1 19 HELIX 11 11 ASP A 194 ASN A 198 5 5 HELIX 12 12 ASP A 201 LYS A 209 1 9 HELIX 13 13 ASP A 217 THR A 224 1 8 HELIX 14 14 PHE A 226 PHE A 228 5 3 HELIX 15 15 LEU A 229 ASN A 237 1 9 HELIX 16 16 ARG A 243 LEU A 261 1 19 HELIX 17 17 ASP A 270 SER A 278 1 9 HELIX 18 18 SER A 291 HIS A 324 1 34 HELIX 19 19 HIS A 324 LEU A 339 1 16 HELIX 20 20 THR A 346 MET A 353 1 8 HELIX 21 21 MET A 353 PHE A 367 1 15 HELIX 22 22 PRO A 397 HIS A 402 1 6 HELIX 23 23 LEU A 415 SER A 420 5 6 HELIX 24 24 GLY A 444 GLN A 461 1 18 SHEET 1 AA 4 VAL A 71 ASP A 76 0 SHEET 2 AA 4 GLN A 79 ILE A 84 -1 O GLN A 79 N ASP A 76 SHEET 3 AA 4 VAL A 393 ILE A 396 1 O VAL A 393 N LEU A 82 SHEET 4 AA 4 LEU A 373 VAL A 376 -1 O LEU A 373 N ILE A 396 SHEET 1 AB 3 VAL A 170 THR A 171 0 SHEET 2 AB 3 VAL A 490 SER A 495 -1 O LEU A 491 N VAL A 170 SHEET 3 AB 3 PHE A 463 LYS A 466 -1 O SER A 464 N GLU A 494 SHEET 1 AC 2 VAL A 381 ILE A 383 0 SHEET 2 AC 2 MET A 386 ILE A 388 -1 O MET A 386 N ILE A 383 LINK SG CYS A 442 FE HEM A1500 1555 1555 2.25 LINK FE HEM A1500 N22 PKT A1600 1555 1555 2.01 CISPEP 1 ILE A 473 PRO A 474 0 -5.02 SITE 1 AC1 21 ARG A 105 ILE A 118 SER A 119 TRP A 126 SITE 2 AC1 21 ARG A 130 PHE A 137 ALA A 305 THR A 309 SITE 3 AC1 21 VAL A 313 ALA A 370 LEU A 373 ARG A 375 SITE 4 AC1 21 PRO A 434 PHE A 435 GLY A 436 SER A 437 SITE 5 AC1 21 ARG A 440 ASN A 441 CYS A 442 GLY A 444 SITE 6 AC1 21 PKT A1600 SITE 1 AC2 9 ARG A 105 PHE A 108 SER A 119 LEU A 211 SITE 2 AC2 9 PHE A 304 ALA A 305 THR A 309 ILE A 369 SITE 3 AC2 9 HEM A1500 CRYST1 78.138 101.332 127.966 90.00 90.00 90.00 I 2 2 2 8 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.012798 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009869 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007815 0.00000